Imagine yourself shopping in a grocery store with a good friend who happens to be a chemist. Struggling to choose between the many different types of tomatoes in front of you, you pick one up, turn to your friend, and ask her if she thinks the tomato is organic. Your friend simply chuckles and replies, "Of course it's organic!" without even looking at how the fruit was grown. Why the amused reaction? Your friend is highlighting a simple difference in vocabulary. To a chemist, the term organic refers to any compound in which hydrogen is bonded to carbon. Tomatoes (like all plants) are abundant in organic compounds – thus your friend's laughter. In modern agriculture, however, organic has come to mean food items grown or raised without the use of chemical fertilizers, pesticides, or other additives.

So who is correct? You both are. Both uses of the word are correct, though they mean different things in different contexts. There are, of course, lots of words that have more than one meaning (like bat, for example), but multiple meanings can be especially confusing when two meanings convey very different ideas and are specific to one field of study.

Scientific theories

The term theory also has two meanings, and this double meaning often leads to confusion. In common language, the term theory generally refers to speculation or a hunch or guess. You might have a theory about why your favorite sports team isn't playing well, or who ate the last cookie from the cookie jar. But these theories do not fit the scientific use of the term. In science, a theory is a well-substantiated and comprehensive set of ideas that explains a phenomenon in nature. A scientific theory is based on large amounts of data and observations that have been collected over time. Scientific theories can be tested and refined by additional research, and they allow scientists to make predictions. Though you may be correct in your hunch, your cookie jar conjecture doesn't fit this more rigorous definition.

All scientific disciplines have well-established, fundamental theories. For example, atomic theory describes the nature of matter and is supported by multiple lines of evidence from the way substances behave and react in the world around us (see our series on Atomic Theory). Plate tectonic theory describes the large scale movement of the outer layer of the Earth and is supported by evidence from studies about earthquakes, magnetic properties of the rocks that make up the seafloor, and the distribution of volcanoes on Earth (see our series on Plate Tectonic Theory). The theory of evolution by natural selection, which describes the mechanism by which inheritedtraits that affect survivability or reproductive success can cause changes in living organisms over generations, is supported by extensive studies of DNA, fossils, and other types of scientific evidence (see our Charles Darwin series for more information). Each of these major theories guides and informs modern research in those fields, integrating a broad, comprehensive set of ideas.

So how are these fundamental theories developed, and why are they considered so well supported? Let's take a closer look at some of the data and research supporting the theory of natural selection to better see how a theory develops.

Comprehension Checkpoint

A theory is simply an educated guess made by a scientist.

a.true

b.false

The development of a scientific theory: Evolution and natural selection

The theory of evolution by natural selection is sometimes maligned as Charles Darwin's speculation on the origin of modern life forms. However, evolutionary theory is not speculation. While Darwin is rightly credited with first articulating the theory of natural selection, his ideas built on more than a century of scientific research that came before him, and are supported by over a century and a half of research since.

The Fixity Notion: Linnaeus

Figure 1: Cover of the 1760 edition of Systema Naturae.

Research about the origins and diversity of life proliferated in the 18th and 19th centuries. Carolus Linnaeus, a Swedish botanist and the father of modern taxonomy (see our module Taxonomy I for more information), was a devout Christian who believed in the concept of Fixity of Species, an idea based on the biblical story of creation. The Fixity of Species concept said that each species is based on an ideal form that has not changed over time. In the early stages of his career, Linnaeus traveled extensively and collected data on the structural similarities and differences between different species of plants. Noting that some very different plants had similar structures, he began to piece together his landmark work, Systema Naturae, in 1735 (Figure 1). In Systema, Linnaeus classified organisms into related groups based on similarities in their physical features. He developed a hierarchical classificationsystem, even drawing relationships between seemingly disparate species (for example, humans, orangutans, and chimpanzees) based on the physical similarities that he observed between these organisms. Linnaeus did not explicitly discuss change in organisms or propose a reason for his hierarchy, but by grouping organisms based on physical characteristics, he suggested that species are related, unintentionally challenging the Fixity notion that each species is created in a unique, ideal form.

The age of Earth: Leclerc and Hutton

Also in the early 1700s, Georges-Louis Leclerc, a French naturalist, and James Hutton, a Scottish geologist, began to develop new ideas about the age of the Earth. At the time, many people thought of the Earth as 6,000 years old, based on a strict interpretation of the events detailed in the Christian Old Testament by the influential Scottish Archbishop Ussher. By observing other planets and comets in the solar system, Leclerc hypothesized that Earth began as a hot, fiery ball of molten rock, mostly consisting of iron. Using the cooling rate of iron, Leclerc calculated that Earth must therefore be at least 70,000 years old in order to have reached its present temperature.

Hutton approached the same topic from a different perspective, gathering observations of the relationships between different rock formations and the rates of modern geological processes near his home in Scotland. He recognized that the relatively slow processes of erosion and sedimentation could not create all of the exposed rock layers in only a few thousand years (see our module The Rock Cycle). Based on his extensive collection of data (just one of his many publications ran to 2,138 pages), Hutton suggested that the Earth was far older than human history – hundreds of millions of years old.

While we now know that both Leclerc and Hutton significantly underestimated the age of the Earth (by about 4 billion years), their work shattered long-held beliefs and opened a window into research on how life can change over these very long timescales.

Fossil studies lead to the development of a theory of evolution: Cuvier

Figure 2: Illustration of an Indian elephant jaw and a mammoth jaw from Cuvier's 1796 paper.

With the age of Earth now extended by Leclerc and Hutton, more researchers began to turn their attention to studying past life. Fossils are the main way to study past life forms, and several key studies on fossils helped in the development of a theory of evolution. In 1795, Georges Cuvier began to work at the National Museum in Paris as a naturalist and anatomist. Through his work, Cuvier became interested in fossils found near Paris, which some claimed were the remains of the elephants that Hannibal rode over the Alps when he invaded Rome in 218 BCE. In studying both the fossils and living species, Cuvier documented different patterns in the dental structure and number of teeth between the fossils and modern elephants (Figure 2) (Horner, 1843). Based on these data, Cuvier hypothesized that the fossil remains were not left by Hannibal, but were from a distinct species of animal that once roamed through Europe and had gone extinct thousands of years earlier: the mammoth. The concept of species extinction had been discussed by a few individuals before Cuvier, but it was in direct opposition to the Fixity of Species concept – if every organism were based on a perfectly adapted, ideal form, how could any cease to exist? That would suggest it was no longer ideal.

While his work provided critical evidence of extinction, a key component of evolution, Cuvier was highly critical of the idea that species could change over time. As a result of his extensive studies of animal anatomy, Cuvier had developed a holistic view of organisms, stating that the

number, direction, and shape of the bones that compose each part of an animal's body are always in a necessary relation to all the other parts, in such a way that ... one can infer the whole from any one of them ...

In other words, Cuvier viewed each part of an organism as a unique, essential component of the whole organism. If one part were to change, he believed, the organism could not survive. His skepticism about the ability of organisms to change led him to criticize the whole idea of evolution, and his prominence in France as a scientist played a large role in discouraging the acceptance of the idea in the scientific community.

Studies of invertebrates support a theory of change in species: Lamarck

Jean Baptiste Lamarck, a contemporary of Cuvier's at the National Museum in Paris, studied invertebrates like insects and worms. As Lamarck worked through the museum's large collection of invertebrates, he was impressed by the number and variety of organisms. He became convinced that organisms could, in fact, change through time, stating that

... time and favorable conditions are the two principal means which nature has employed in giving existence to all her productions. We know that for her time has no limit, and that consequently she always has it at her disposal.

This was a radical departure from both the fixity concept and Cuvier's ideas, and it built on the long timescale that geologists had recently established. Lamarck proposed that changes that occurred during an organism's lifetime could be passed on to their offspring, suggesting, for example, that a body builder's muscles would be inherited by their children.

As it turned out, the mechanism by which Lamarck proposed that organisms change over time was wrong, and he is now often referred to disparagingly for his "inheritance of acquired characteristics" idea. Yet despite the fact that some of his ideas were discredited, Lamarck established a support for evolutionary theory that others would build on and improve.

Comprehension Checkpoint

To develop theories, scientists most often

a.rely on an accumulation of knowledge developed by many scientists over time.

b.use only their own direct experience and observations.

Rock layers as evidence for evolution: Smith

In the early 1800s, a British geologist and canal surveyor named William Smith added another component to the accumulating evidence for evolution. Smith observed that rock layers exposed in different parts of England bore similarities to one another: These layers (or strata) were arranged in a predictable order, and each layer contained distinct groups of fossils. From this series of observations, he developed a hypothesis that specific groups of animals followed one another in a definite sequence through Earth's history, and this sequence could be seen in the rock layers. Smith's hypothesis was based on his knowledge of geological principles, including the Law of Superposition.

The Law of Superposition states that sediments are deposited in a time sequence, with the oldest sediments deposited first, or at the bottom, and newer layers deposited on top. The concept was first expressed by the Persian scientist Avicenna in the 11th century, but was popularized by the Danish scientist Nicolas Steno in the 17th century. Note that the law does not state how sediments are deposited; it simply describes the relationship between the ages of deposited sediments.

Figure 3: Engraving from William Smith's 1815 monograph on identifying strata by fossils.

Smith backed up his hypothesis with extensive drawings of fossils uncovered during his research (Figure 3), thus allowing other scientists to confirm or dispute his findings. His hypothesis has, in fact, been confirmed by many other scientists and has come to be referred to as the Law of Faunal Succession. His work was critical to the formation of evolutionary theory as it not only confirmed Cuvier's work that organisms have gone extinct, but it also showed that the appearance of life does not date to the birth of the planet. Instead, the fossil record preserves a timeline of the appearance and disappearance of different organisms in the past, and in doing so offers evidence for change in organisms over time.

It was into this world that Charles Darwin entered: Linnaeus had developed a taxonomy of organisms based on their physical relationships, Leclerc and Hutton demonstrated that there was sufficient time in Earth's history for organisms to change, Cuvier showed that species of organisms have gone extinct, Lamarck proposed that organisms change over time, and Smith established a timeline of the appearance and disappearance of different organisms in the geological record.

Figure 4: Title page of the 1859 Murray edition of the Origin of Species by Charles Darwin.

Charles Darwin collected data during his work as a naturalist on the HMS Beagle starting in 1831. He took extensive notes on the geology of the places he visited; he made a major find of fossils of extinct animals in Patagonia and identified an extinct giant ground sloth named Megatherium. He experienced an earthquake in Chile that stranded beds of living mussels above water, where they would be preserved for years to come.

Perhaps most famously, he conducted extensive studies of animals on the Galápagos Islands, noting subtle differences in species of mockingbird, tortoise, and finch that were isolated on different islands with different environmental conditions. These subtle differences made the animals highly adapted to their environments.

This broad spectrum of data led Darwin to propose an idea about how organisms change "by means of natural selection" (Figure 4). But this idea was not based only on his work, it was also based on the accumulation of evidence and ideas of many others before him. Because his proposal encompassed and explained many different lines of evidence and previous work, they formed the basis of a new and robust scientific theory regarding change in organisms – the theory of evolution by natural selection.

Darwin's ideas were grounded in evidence and data so compelling that if he had not conceived them, someone else would have. In fact, someone else did. Between 1858 and 1859, Alfred Russel Wallace, a British naturalist, wrote a series of letters to Darwin that independently proposed natural selection as the means for evolutionary change. The letters were presented to the Linnean Society of London, a prominent scientific society at the time (see our module on Scientific Institutions and Societies). This long chain of research highlights that theories are not just the work of one individual. At the same time, however, it often takes the insight and creativity of individuals to put together all of the pieces and propose a new theory. Both Darwin and Wallace were experienced naturalists who were familiar with the work of others. While all of the work leading up to 1830 contributed to the theory of evolution, Darwin's and Wallace's theory changed the way that future research was focused by presenting a comprehensive, well-substantiated set of ideas, thus becoming a fundamental theory of biological research.

Expanding, testing, and refining scientific theories

Genetics and evolution: Mendel and Dobzhansky

Since Darwin and Wallace first published their ideas, extensive research has tested and expanded the theory of evolution by natural selection. Darwin had no concept of genes or DNA or the mechanism by which characteristics were inherited within a species. A contemporary of Darwin's, the Austrian monk Gregor Mendel, first presented his own landmark study, Experiments in Plant Hybridization, in 1865 in which he provided the basic patterns of genetic inheritance, describing which characteristics (and evolutionary changes) can be passed on in organisms (see our Genetics I module for more information). Still, it wasn't until much later that a "gene" was defined as the heritable unit.

In 1937, the Ukrainian born geneticist Theodosius Dobzhansky published Genetics and the Origin of Species, a seminal work in which he described genes themselves and demonstrated that it is through mutations in genes that change occurs. The work defined evolution as "a change in the frequency of an allele within a gene pool" (Dobzhansky, 1982). These studies and others in the field of genetics have added to Darwin's work, expanding the scope of the theory.

Evolution under a microscope: Lenski

More recently, Dr. Richard Lenski, a scientist at Michigan State University, isolated a single Escherichia coli bacterium in 1989 as the first step of the longest running experimental test of evolutionary theory to date – a true test meant to replicate evolution and natural selection in the lab.

After the single microbe had multiplied, Lenski isolated the offspring into 12 different strains, each in their own glucose-supplied culture, predicting that the genetic make-up of each strain would change over time to become more adapted to their specific culture as predicted by evolutionary theory. These 12 lines have been nurtured for over 40,000 bacterial generations (luckily bacterial generations are much shorter than human generations) and exposed to different selective pressures such as heat, cold, antibiotics, and infection with other microorganisms. Lenski and colleagues have studied dozens of aspects of evolutionary theory with these genetically isolated populations. In 1999, they published a paper that demonstrated that random genetic mutations were common within the populations and highly diverse across different individual bacteria. However, "pivotal" mutations that are associated with beneficial changes in the group are shared by all descendants in a population and are much rarer than random mutations, as predicted by the theory of evolution by natural selection (Papadopoulos et al., 1999).

Punctuated equilibrium: Gould and Eldredge

While established scientific theories like evolution have a wealth of research and evidence supporting them, this does not mean that they cannot be refined as new information or new perspectives on existing data become available. For example, in 1972, biologist Stephen Jay Gould and paleontologist Niles Eldredge took a fresh look at the existing data regarding the timing by which evolutionary change takes place. Gould and Eldredge did not set out to challenge the theory of evolution; rather they used it as a guiding principle and asked more specific questions to add detail and nuance to the theory. This is true of all theories in science: they provide a framework for additional research. At the time, many biologists viewed evolution as occurring gradually, causing small incremental changes in organisms at a relatively steady rate. The idea is referred to as phyletic gradualism, and is rooted in the geological concept of uniformitarianism. After reexamining the available data, Gould and Eldredge came to a different explanation, suggesting that evolution consists of long periods of stability that are punctuated by occasional instances of dramatic change – a process they called punctuated equilibrium.

Like Darwin before them, their proposal is rooted in evidence and research on evolutionary change, and has been supported by multiple lines of evidence. In fact, punctuated equilibrium is now considered its own theory in evolutionary biology. Punctuated equilibrium is not as broad of a theory as natural selection. In science, some theories are broad and overarching of many concepts, such as the theory of evolution by natural selection; others focus on concepts at a smaller, or more targeted, scale such as punctuated equilibrium. And punctuated equilibrium does not challenge or weaken the concept of natural selection; rather, it represents a change in our understanding of the timing by which change occurs in organisms, and a theory within a theory. The theory of evolution by natural selection now includes both gradualism and punctuated equilibrium to describe the rate at which change proceeds.

Comprehension Checkpoint

Observation and research can challenge existing ideas in science.

a.true

b.false

Hypotheses and laws: Other scientific concepts

One of the challenges in understanding scientific terms like theory is that there is not a precise definition even within the scientific community. Some scientists debate over whether certain proposals merit designation as a hypothesis or theory, and others mistakenly use the terms interchangeably. But there are differences in these terms. A hypothesis is a proposed explanation for an observable phenomenon. Hypotheses, just like theories, are based on observations from research. For example, LeClerc did not hypothesize that Earth had cooled from a molten ball of iron as a random guess; rather, he developed this hypothesis based on his observations of information from meteorites.

A scientist often proposes a hypothesis before research confirms it as a way of predicting the outcome of study to help better define the parameters of the research. LeClerc's hypothesis allowed him to use known parameters (the cooling rate of iron) to do additional work. A key component of a formal scientific hypothesis is that it is testable and falsifiable. For example, when Richard Lenski first isolated his 12 strains of bacteria, he likely hypothesized that random mutations would cause differences to appear within a period of time in the different strains of bacteria. But when a hypothesis is generated in science, a scientist will also make an alternative hypothesis, an explanation that explains a study if the data do not support the original hypothesis. If the different strains of bacteria in Lenski's work did not diverge over the indicated period of time, perhaps the rate of mutation was slower than first thought.

So you might ask, if theories are so well supported, do they eventually become laws? The answer is no – not because they aren't well-supported, but because theories and laws are two very different things. Laws describe phenomena, often mathematically. Theories, however, explain phenomena. For example, in 1687 Isaac Newton proposed a Theory of Gravitation, describing gravity as a force of attraction between two objects. As part of this theory, Newton developed a Law of Universal Gravitation that explains how this force operates. This law states that the force of gravity between two objects is inversely proportional to the square of the distance between those objects. Newton's Law does not explain why this is true, but it describes how gravity functions (see our Gravity: Newtonian Relationships module for more detail). In 1916, Albert Einstein developed his theory of general relativity to explain the mechanism by which gravity has its effect. Einstein's work challenges Newton's theory, and has been found after extensive testing and research to more accurately describe the phenomenon of gravity. While Einstein's work has replaced Newton's as the dominant explanation of gravity in modern science, Newton's Law of Universal Gravitation is still used as it reasonably (and more simply) describes the force of gravity under many conditions. Similarly, the Law of Faunal Succession developed by William Smith does not explain whyorganisms follow each other in distinct, predictable ways in the rock layers, but it accurately describes the phenomenon.

Theories, hypotheses, and laws are not simply important components of science, they drive scientific progress. For example, evolutionary biology now stands as a distinct field of science that focuses on the origins and descent of species. Geologists now rely on plate tectonics as a conceptual model and guiding theory when they are studying processes at work in Earth's crust. And physicists refer to atomic theory when they are predicting the existence of subatomic particles yet to be discovered. This does not mean that science is "finished," or that all of the important theories have been discovered already. Like evolution, progress in science happens both gradually and in short, dramatic bursts. Both types of progress are critical for creating a robust knowledge base with data as the foundation and scientific theories giving structure to that knowledge.

Summary

Theories are not based on one scientist's work but on an accumulation of evidence and ideas from many scientists over time. This module discusses how scientific theories are built and revised. It uses the development of the theory of evolution through natural selection to illustrate how theories are built through a process of testing, expanding, and refining.

Key Concepts

A scientific theory is an explanation inferred from multiple lines of evidence for some broad aspect of the natural world and is logical, testable, and predictive.

As new evidence comes to light, or new interpretations of existing data are proposed, theories may be revised and even change; however, they are not tenuous or speculative.

A scientific hypothesis is an inferred explanation of an observation or research finding; while more exploratory in nature than a theory, it is based on existing scientific knowledge.

A scientific law is an expression of a mathematical or descriptive relationship observed in nature.

Horner, W. E. (1843). Remarks on the dental system of the mastodon, with an account of some lower jaws in Mr. Koch's collection, St. Louis, Missouri, where there is a solitary tusk on the right side. Transactions of the American Philosophical Society, 8, 53-59.

Johnson, S. (2008). The invention of air: A story of science, faith, revolution, and the birth of America. New York: Riverhead Books.